This script uses the data.frame “data”, loaded from s01.RData. That is, all rows with C==“C” has been excluded for exploratory data analysis.
# ------------------------------------------------------------------
# Prepare environment
# ------------------------------------------------------------------
# load packages
source(file = file.path("Scripts","Setup","setup01_projectPackages.R"))
# load output from s01_DatasetPrep.R
load(file=file.path("Scripts","s01.RData"))
# White background in plots
theme_set(theme_bw()) # to be replaced with a azTheme
update_geom_defaults("point", list(shape = 1))
Are the plots and tables also being written to file?
## [1] TRUE
The markdown/latex notation for tables does not work for html output. Notified the authour of pixidust.
| Characteristic | mean (SD) [range] | Missing (N (%)) |
|---|---|---|
| Age (yrs) | 39.000 (8.590), [17.000-60.0] | 0 (0.00) |
| Serum creatinine (mg/dL) | 0.835 (0.166), [0.459-1.3] | 4 (6.67) |
| eGFR (mL/min/1.73m^2^) | 99.400 (32.200), [46.500-212.0] | 4 (6.67) |
| Body weight (kg) | 75.200 (11.400), [56.000-102.0] | 2 (3.33) |
| Body height (cm) | 176.000 (11.100), [152.000-208.0] | 2 (3.33) |
| Body mass index (kg/m^2^) | 24.300 (3.900), [17.100-35.2] | 4 (6.67) |
| Characteristic | Category | N (%) |
|---|---|---|
| Sex | Female | 26 (43.30) |
| Male | 34 (56.70) | |
| Race | White | 19 (31.70) |
| Black/African American | 9 (15.00) | |
| Asian | 14 (23.30) | |
| Other | 18 (30.00) | |
| Ethnicity | Hispanic/Latino | 11 (18.30) |
| Not Hispanic/Latino | 17 (28.30) | |
| Not Reported | 16 (26.70) | |
| Unknown | 16 (26.70) | |
| Renal impairment | Normal | 33 (55.00) |
| Mild | 20 (33.30) | |
| Moderate | 3 (5.00) | |
| Missing | 4 (6.67) |
| Study | Characteristic | mean (SD) [range] | Missing (N (%)) |
|---|---|---|---|
| d0000c0001 | Age (yrs) | 41.100 (7.800), [27.000-60.00] | 0 (0.00) |
| Serum creatinine (mg/dL) | 0.796 (0.129), [0.484-1.08] | 2 (6.67) | |
| eGFR (mL/min/1.73m^2^) | 106.000 (29.300), [63.900-198.00] | 2 (6.67) | |
| Body weight (kg) | 76.600 (11.100), [56.000-102.00] | 1 (3.33) | |
| Body height (cm) | 180.000 (11.800), [159.000-208.00] | 2 (6.67) | |
| BMI (kg/m^2^) | 23.700 (3.570), [17.200-29.80] | 3 (10.00) | |
| d0000c0002 | Age (yrs) | 36.800 (8.930), [17.000-51.00] | 0 (0.00) |
| Serum creatinine (mg/dL) | 0.874 (0.191), [0.459-1.30] | 2 (6.67) | |
| eGFR (mL/min/1.73m^2^) | 92.700 (34.100), [46.500-212.00] | 2 (6.67) | |
| Body weight (kg) | 73.900 (11.800), [57.000-99.00] | 1 (3.33) | |
| Body height (cm) | 172.000 (9.160), [152.000-198.00] | 0 (0.00) | |
| BMI (kg/m^2^) | 24.800 (4.170), [17.100-35.20] | 1 (3.33) |
| Study | Characteristic | Category | N (%) |
|---|---|---|---|
| d0000c0001 | Sex | Female | 8 (26.70) |
| Male | 22 (73.30) | ||
| Race | White | 11 (36.70) | |
| Black/African American | 3 (10.00) | ||
| Asian | 8 (26.70) | ||
| Other | 8 (26.70) | ||
| Ethnicity | Hispanic/Latino | 7 (23.30) | |
| Not Hispanic/Latino | 8 (26.70) | ||
| Not Reported | 7 (23.30) | ||
| Unknown | 8 (26.70) | ||
| Renal impairment | Normal | 19 (63.30) | |
| Mild | 9 (30.00) | ||
| Missing | 2 (6.67) | ||
| d0000c0002 | Sex | Female | 18 (60.00) |
| Male | 12 (40.00) | ||
| Race | White | 8 (26.70) | |
| Black/African American | 6 (20.00) | ||
| Asian | 6 (20.00) | ||
| Other | 10 (33.30) | ||
| Ethnicity | Hispanic/Latino | 4 (13.30) | |
| Not Hispanic/Latino | 9 (30.00) | ||
| Not Reported | 9 (30.00) | ||
| Unknown | 8 (26.70) | ||
| Renal impairment | Normal | 14 (46.70) | |
| Mild | 11 (36.70) | ||
| Moderate | 3 (10.00) | ||
| Missing | 2 (6.67) |
| Dose | Characteristic | mean (SD) [range] | Missing (N (%)) |
|---|---|---|---|
| 25 | Age (yrs) | 39.700 (8.200), [28.000-51.000] | 0 (0.00) |
| Serum creatinine (mg/dL) | 0.895 (0.237), [0.459-1.300] | 1 (6.67) | |
| eGFR (mL/min/1.73m^2^) | 90.900 (41.500), [46.500-212.000] | 1 (6.67) | |
| Body weight (kg) | 74.700 (10.400), [59.000-97.000] | 0 (0.00) | |
| Body height (cm) | 171.000 (6.280), [160.000-181.000] | 0 (0.00) | |
| BMI (kg/m^2^) | 25.500 (3.720), [21.300-35.200] | 0 (0.00) | |
| 100 | Age (yrs) | 40.900 (7.530), [28.000-51.000] | 0 (0.00) |
| Serum creatinine (mg/dL) | 0.800 (0.150), [0.484-1.080] | 1 (6.67) | |
| eGFR (mL/min/1.73m^2^) | 108.000 (35.200), [63.900-198.000] | 1 (6.67) | |
| Body weight (kg) | 80.200 (12.900), [56.000-102.000] | 1 (6.67) | |
| Body height (cm) | 179.000 (10.300), [159.000-196.000] | 1 (6.67) | |
| BMI (kg/m^2^) | 24.700 (3.370), [20.400-29.800] | 2 (13.30) | |
| 150 | Age (yrs) | 41.300 (8.320), [27.000-60.000] | 0 (0.00) |
| Serum creatinine (mg/dL) | 0.792 (0.108), [0.659-0.989] | 1 (6.67) | |
| eGFR (mL/min/1.73m^2^) | 104.000 (23.200), [64.700-137.000] | 1 (6.67) | |
| Body weight (kg) | 73.200 (8.090), [60.000-87.000] | 0 (0.00) | |
| Body height (cm) | 181.000 (13.400), [166.000-208.000] | 1 (6.67) | |
| BMI (kg/m^2^) | 22.800 (3.620), [17.200-29.100] | 1 (6.67) | |
| 300 | Age (yrs) | 33.900 (8.910), [17.000-50.000] | 0 (0.00) |
| Serum creatinine (mg/dL) | 0.854 (0.138), [0.542-1.120] | 1 (6.67) | |
| eGFR (mL/min/1.73m^2^) | 94.400 (26.100), [64.200-176.000] | 1 (6.67) | |
| Body weight (kg) | 73.000 (13.500), [57.000-99.000] | 1 (6.67) | |
| Body height (cm) | 173.000 (11.500), [152.000-198.000] | 0 (0.00) | |
| BMI (kg/m^2^) | 24.000 (4.630), [17.100-32.900] | 1 (6.67) |
| Dose | Characteristic | Category | N (%) |
|---|---|---|---|
| 25 | Sex | Female | 8 (53.30) |
| Male | 7 (46.70) | ||
| Race | White | 5 (33.30) | |
| Black/African American | 2 (13.30) | ||
| Asian | 3 (20.00) | ||
| Other | 5 (33.30) | ||
| Ethnicity | Hispanic/Latino | 2 (13.30) | |
| Not Hispanic/Latino | 4 (26.70) | ||
| Not Reported | 5 (33.30) | ||
| Unknown | 4 (26.70) | ||
| Renal impairment | Normal | 7 (46.70) | |
| Mild | 4 (26.70) | ||
| Moderate | 3 (20.00) | ||
| Missing | 1 (6.67) | ||
| 100 | Sex | Female | 4 (26.70) |
| Male | 11 (73.30) | ||
| Race | White | 5 (33.30) | |
| Black/African American | 3 (20.00) | ||
| Asian | 4 (26.70) | ||
| Other | 3 (20.00) | ||
| Ethnicity | Hispanic/Latino | 6 (40.00) | |
| Not Hispanic/Latino | 2 (13.30) | ||
| Not Reported | 2 (13.30) | ||
| Unknown | 5 (33.30) | ||
| Renal impairment | Normal | 9 (60.00) | |
| Mild | 5 (33.30) | ||
| Missing | 1 (6.67) | ||
| 150 | Sex | Female | 4 (26.70) |
| Male | 11 (73.30) | ||
| Race | White | 6 (40.00) | |
| Asian | 4 (26.70) | ||
| Other | 5 (33.30) | ||
| Ethnicity | Hispanic/Latino | 1 (6.67) | |
| Not Hispanic/Latino | 6 (40.00) | ||
| Not Reported | 5 (33.30) | ||
| Unknown | 3 (20.00) | ||
| Renal impairment | Normal | 10 (66.70) | |
| Mild | 4 (26.70) | ||
| Missing | 1 (6.67) | ||
| 300 | Sex | Female | 10 (66.70) |
| Male | 5 (33.30) | ||
| Race | White | 3 (20.00) | |
| Black/African American | 4 (26.70) | ||
| Asian | 3 (20.00) | ||
| Other | 5 (33.30) | ||
| Ethnicity | Hispanic/Latino | 2 (13.30) | |
| Not Hispanic/Latino | 5 (33.30) | ||
| Not Reported | 4 (26.70) | ||
| Unknown | 4 (26.70) | ||
| Renal impairment | Normal | 7 (46.70) | |
| Mild | 7 (46.70) | ||
| Missing | 1 (6.67) |
The diagonal graphs show histograms of each covariate. The lower off-diagonal graphs are scatter plots of observations (black open circles) with linear regression (black line) and its 95% confidence interval (grey shaded area). The lower off-diagonal graphs show the Pearson’s correlation coefficient. The graphs are displayed in red if the Pearson’s correlation coefficient is > 0.4.
The diagonal graphs show bar charts of each covariate. The off-diagonal graphs show the correlation between covariate categories: the black point is a visual reference point, and the numbers are percentage of subjects of a covariate split by the groups of the other covariate. For example, the bottom left graph show that within the group with normal renal function, 19% are female and 81% are male (numbers aligned left of the reference point). Similarly, within the group of females, 29% have normal, 36% have mild, 21% have moderate renal impairment and 14% is missing information (numbers aligned above the reference point). NA refers to not available, i.e., missing.
## Warning in dev(file = filename, width = dim[1], height = dim[2], ...):
## failed to load cairo DLL
The black line within the box shows the median and the box’s upper and lower edges show the inter quartile range (IQR). Whiskers extend to the highest value that is within 1.5*IQR. Data beyond the end of the whiskers are outliers and plotted as points. NA refers to not available, i.e., missing.
The black line within the box shows the median and the box’s upper and lower edges show the inter quartile range (IQR). Whiskers extend to the highest value that is within 1.5*IQR. Data beyond the end of the whiskers are outliers and plotted as points.
The diagonal graphs show bar charts of each covariate. The off-diagonal graphs show the correlation between covariate categories: the black point is a visual reference point, and the numbers are percentage of subjects of a variable split by the groups of the other variable. NA refers to not available, i.e., missing. See also example text for categorical covariate correlation above.
The lines connect data from one individual. Ticks indicate all individual records of the covariate in the dataset. The blue line with shaded area is a loess smooth and its 95% confidence interval indicating any overall trends in changes of covariate values over time after first dose.
## quartz_off_screen
## 2
The lines are a step function connecting data from one individual. Ticks indicate all individual records of the covariate in the dataset.
## quartz_off_screen
## 2
Ticks indicate all individual records of the covariate in the dataset.
## quartz_off_screen
## 2
The lines are a step function connecting data from one individual. Ticks indicate all individual records of the covariate in the dataset.
## quartz_off_screen
## 2